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  • BIRCH: Comprehensive bioinfo. system - Support tickets

    Submit | Open tickets | Closed tickets

    [ Ticket #1214 ] chooseviewer.py fails to open html files on MacOSX
    Date:
    04/11/17 13:25
    Submitted by:
    B_Fristensky
    Assigned to:
    B_Fristensky
    Category:
    Unset
    Priority:
    8
    Ticket group:
    Bug
    Resolution:
    Resolved
    Summary:
    chooseviewer.py fails to open html files on MacOSX
    Original submission:
    Programs that call chooseviewer.py to view documents fail to open the .html files. Of particular note are calls from blblastout.py to open BLAST reports sent to html files.

    This worked on Linux, but not MacOSX.

    The htmlfiles were being created, and chooseviewer.py was copying them to files named chooseviewerxxxxxx.html, but the application to read them was not being launched.

    The problem seems to be that on OSX the way to over a file is

    open -a appname

    where appname is the name of the program eg. firefox

    Chooseviewer reads the command to use for a particular file from an environment variable. On linux, these are always single non-blank strings, but on OSX they are multi-token strings eg.

    open -a firefox

    chooseviewer.py has been modified to first parst the results of environment variables such as $BL_Browser into a list of tokens, and then append the target filename to that list. That list then gets sent to subprocess.Popen to run the command.

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    Ticket change history
    Field Old value Date By
    status_id Open 05/02/17 16:10 B_Fristensky
    resolution_id Not Resolved 05/02/17 16:10 B_Fristensky
    close_date 12/31/69 19:00 05/02/17 16:10 B_Fristensky
    status_id Pending 04/11/17 13:25 B_Fristensky
    priority 5 04/11/17 13:25 B_Fristensky
    assigned_to unset 04/11/17 13:25 B_Fristensky
    resolution_id Unset 04/11/17 13:25 B_Fristensky

     

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